Tenant responsible for replacing old carpet after move-out?

[Jane Lynn]

We purchased the house in June 2017 and had the carpets cleaned prior to the tenant moving in. We are not sure how old it is, but there were obviously were pets prior with the last homeowner. The basement was heavily stained. We cleaned them however. Several months into the lease, there was a water leak in the basement and the carpet in the basement had to be replaced. We chose vinyl. The carpet on the second floor was in fine shape prior to their move it. They had two dogs and two dogs that were service animals that we couldnt do anything about. They are "invisible". The carpet has been soiled and they hired a carpet cleaner, but some of the spots are coming back. the wood floor on the first level has also been scratched and their is a slight urine smell. What should our course of action be? We did take a deposit for the two dogs and charged $125 pet rent each month.